For the first time, scientists report a vampire fish attached to the body of an Amazonian thorny catfish. Very unusually, the candirus were attached close to the lateral bone plates, rather than the gills, where they are normally found. Since the hosts were not badly harmed, and the candirus apparently derived no food benefit, scientists believe this association is commensalistic rather than parasitic. The research is published in the open-access journal Acta Ichthyologica et Piscatoria.
Guest blog post by Chiara C. F. Lubich, André R. Martins, Carlos E. C. Freitas, Lawrence E. Hurd and Flávia K. Siqueira-Souza
The Amazon River Basin is home to about 15% of all freshwater fish species known to science, and an estimated 40% yet to be named. These include some of the most bizarre fishes: the vampire fishes, locally known as candiru, members of the catfish subfamily Vandelliinae.). They survive by attaching themselves to the bodies of other fish and sucking on their blood, hence their common name. Yet, it was only recently that we found out that one candiru species, belonging to the genus Paracanthopoma,seems to be making use of its host in quite a different way.
During a sampling study of freshwater fish fauna in a lake of the Demeni River Basin, a left bank tributary of the Negro River, we found candirus attached to the surface of the body of an Amazonian species of a thorny catfish. By the end of the survey, we had observed a total of twenty candirus attached to the outside of the bodies of nine larger Doras phlyzakion, one or two per host. Very unusually, the candirus were attached close to the lateral bone plates, rather than the gills, where these fish are normally found.
As a result of these observations, we recently published the first record of a candiru attached to the body surface of an Amazonian thorny catfish in an article in the open-access scholarly journal Acta Ichthyologica et Piscatoria.
Vampire fish have long and robust snouts, with strong dentary teeth that help them stay attached to the epidermis of their host and feed on its blood. However, when we performed a macroscopic analysis of the stomach contents of the preserved Paracanthopoma specimens, we were surprised to find no coagulated blood, nor flesh, skin or mucus. This might indicate an interaction between parasite and host that is more benign than usually attributed to vampire fish.
We believe the association between candiru and host in this case might be commensalistic (where one organism benefits from another without harming it), rather than parasitic, because the hosts were not badly harmed, and the candiru apparently derived no food benefit.
But what else would they seek on the back of Amazonian thorny catfish? One explanation could be that, since candirus are tiny and nearly transparent, they might be avoiding getting noticed by visual predators by riding on larger fish. Another hypothesis is that they could be using their big cousins to transport them over longer distances that they wouldn’t be able to cover themselves, eventually making it to safety or new food sources.
Lubich CCF, Martins AR, Freitas CEC, Hurd LE, Siqueira-Souza FK (2021) A candiru, Paracanthopoma sp. (Siluriformes: Trichomycteridae), associated with a thorny catfish, Doras phlyzakion (Siluriformes: Doradidae), in a tributary of the middle Rio Negro, Brazilian Amazon. Acta Ichthyologica et Piscatoria 51(3): 241-244. https://doi.org/10.3897/aiep.51.e64324
Have you ever seen a one-centimetre-long jumping critter in a leaflitter or close to a pond or a stream and thought that it is some juvenile insect? What you saw was probably an adult pygmy grasshopper, member of the family Tetrigidae. There are more than 2000 described species of those minute jumping insects, and this peculiar family has been around for more than 230 million years, meaninng that pygmies said both ‘hi’ and ‘bye’ to dinosaurs. And yet, we know more about dinosaurs than we do about pygmy grasshoppers.
“(…) pronotum often takes on various extreme modifications, giving to the insects a most grotesque or bizarre appearance (…)”
quote from Hancock, Joseph Lane (1907) Orthoptera fam. Acridiidae, subfam Tetriginae. Genera Insectorum.
Have you ever seen a one-centimetre-long jumping critter in a leaflitter or close to a pond or a stream and thought that it is some juvenile insect? Well, I must disappoint you. What you saw was probably an adult pygmy grasshopper, member of the family Tetrigidae. There are more than 2000 described species of those minute jumping insects, and this peculiar family has been around for more than 230 million years, meaninng that pygmies said both ‘hi’ and ‘bye’ to dinosaurs. And yet, we know more about dinosaurs than we do about pygmy grasshoppers.
Most of the research you can find out there is probably based on genera Tetrix and Paratettix in Europe or Northern America (Adžić et al. 2021). Species of Northern America (Nearctic region, 35 species) and Europe (W Palearctic region, 11 species) are indeed best known from the standpoint of natural history, even though they represent only about 2% of the diversity. Here is the list of 19 species that are most often observed by amateur naturalists on the iNaturalist platform (Table 1) and as you can see 12 out of 19 species are indeed from Europe and Northern America. Because of that, let us focus on awesome neglected diversity in the tropics.
N of observations
Indochina and islands of SE Asia
W Palearctic: Mediterranean
S Nearctic to N Neotropics
Java, Sumatra, Bali
Table 1. Well-known Tetrigidae species. Pygmy grasshoppers with more than 25 Research-Grade observations in iNaturalist, together with their distribution briefly explained.
Why do I mention the iNaturalist platform? Because I think it is the future of zoology, especially of faunistics. Never before have we been able to simultaneously gather so much data from so many different places. I started using Flickr some time ago to search for photos of unidentified rare pygmy grasshoppers. I did find many rare species, and what is even crazier, species that were not known to science. I’ll try to present you with a glimpse of the diversity I found online, so maybe some new students or amateurs will contribute, as they did with Paraselina brunneri, after the study was published in ZooKeys.
It seems that “rare” species from Australia are not so rare after all
Many new records ofParaselina brunneri and Selivinga tribulata can now be found online, thanks to a study published with ZooKeys.
Enjoy some selected awesome places and selected amazing taxa that inhabit those places. Emphasis is given on the extremely rare and weird-looking, or as Hancock called them, bizarre and grotesque species. Those with leaf-like morphology, spines, warts, undulations, or horns. Enjoy a short voyage from the rainforests of Madagascar through the humid forests of Australia, New Guinea, Borneo, and finally the Atlantic Forest of Brazil.
Madagascar is home to some of the largest and most colourful species of Tetrigidae in whole world
Very peculiar are the species of the genera Holocerusand Notocerus, both of which were discussed in studies published in ZooKeys. Finally, one can find photographs of these beauties identified to species level.
Interesting fact about those large pygmy grasshoppers: When I visited the rainforests of Madagascar, I observed one Holocerus devriesei and took photos of it. The insect then took flight far away in the rainforest. Who could think that an animal with such a large back spines could be such a skilful flier! The same is maybe true for Notocerus.
Not all pygmy grasshoppers are large and colourful
Some species, like the Pymgy unicorns of Southern America are small but still interesting. Metopomystrum muriciense was described with ZooKeys from the Atlantic rainforests of Murici, Brazil, in 2017.
Some pygmy grasshoppers are weird
Giraffehoppers from New Guinea are among the most unique pygmy grasshoppers. Many species can be differentiated by the antennal shape, and maybe by face coloration. Those are very visual animals, and antennae and colours might be used for courtship (Tumbrinck & Skejo 2017).
For young entomologists: How did I decide to study pygmy grasshoppers?
No true biology student knows what she or he wants to study and which direction to take. With me, it was pretty much the same thing. Systematics caught my attention during primary and high school, and I always had a tendency to systematically compare data. My first idea was to study snakes, as I was amazed by shield-tailed snakes (Uropeltidae) and blind snakes (Scolecophidia), about whom I have read a lot. Unfortunately, I never saw representatives of those snake groups, but fortunately, there were a lot of animals that I had seen, and with whom I was more familiar in the field. Among them, there were grasshoppers and crickets (order Orthoptera). Together with Fran Rebrina, my friend and fellow student, I started the first systematic research of Orthoptera of Croatia and the Balkans. Our study on two Croatian endemic species, Rhacocleis buchichii and Barbitistes kaltenbachi, was published with ZooKeys last year.
In the first years of our Orthoptera studies (2011-2012), I never saw a single pygmy grasshopper in Croatia. I remember it as if it was yesterday when Fran and I asked our senior colleague, Ivan Budinski (BIOM, Sinj), where we could find Tetrigidae, and he confidently said that they are to be found around water. Peruća lake near the city of Vrlika was he place where I saw pygmy grasshoppers, namely Tetrix depressa and Tetrix ceperoi, for the first time ever. I could not believe that there were grasshoppers whose lifecycle is water dependent in any way, so I kept researching them, contacting leading European orthopterists familiar with them (Hendrik Devriese, Axel Hochkirch, Josef Tumbrinck), and checking all the museum collections where I could enter. The encounter on the shores of Peruća was the moment that determined my career as an entomologist. After I discovered specimens of the extremely rare Tetrix transsylvanica in Croatian Natural History Museum (HPM – Hrvatski Prirodoslovni Muzej, Zagreb) in 2013 (Skejo et al. 2014), and after a serendipitous discovery of a new Arulenus species (Skejo & Caballero 2016), I just decided that maybe this interesting group was understudied and required systematic research, and here I am in 2021, regularly publishing on this very group.
Mathieu É, Pavlović M, Skejo J (2021) The true colours of the Formidable Pygmy Grasshopper (Notocerus formidabilis Günther, 1974) from the Sava region (Madagascar). ZooKeys 1042: 41-50. https://doi.org/10.3897/zookeys.1042.66381
Silva DSM, Josip Skejo, Pereira MR, De Domenico FC, Sperber CF (2017) Comments on the recent changes in taxonomy of pygmy unicorns, with description of a new species of Metopomystrum from Brazil (Insecta, Tetrigidae, Cleostratini, Miriatrini). ZooKeys 702: 1-18. https://doi.org/10.3897/zookeys.702.13981
Skejo J, Connors M, Hendriksen M, Lambert N, Chong G, McMaster I, Monaghan N, Rentz D, Richter R, Rose K, Franjević D (2020) Online social media tells a story of Anaselina, Paraselina, and Selivinga (Orthoptera, Tetrigidae), rare Australian pygmy grasshoppers. ZooKeys 948: 107-119. https://doi.org/10.3897/zookeys.948.52910
Skejo J, Medak K, Pavlović M, Kitonić D, Miko RJC, Franjević D (2020) The story of the Malagasy devils (Orthoptera, Tetrigidae): Holocerus lucifer in the north and H. devriesei sp. nov. in the south? ZooKeys 957: 1-15. https://doi.org/10.3897/zookeys.957.52565
Tumbrinck, J & Skejo, J. (2027) Taxonomic and biogeographic revision of the New Guinean genus Ophiotettix Walker, 1871 (Tetrigidae: Metrodorinae: Ophiotettigini trib. nov.), with the descriptions of 33 new species. In Telnov D, Barclay MVL, Pauwels OS (Eds) Biodiversity, biogeography and nature conservation in Wallacea and New Guinea (Volume III). The Entomological Society of Latvia, Riga, Latvia, 525-580.
One of the main threats to biodiversity conservation is not recognizing the uniqueness of species – without a formal name, a species cannot be protected properly. Tardigrades – microorganisms also known as water bears or moss piglets – are no exception. When we were faced with two new species, we took the chance to describe them and add a small piece of information to the biodiversity of those tiny animals.
Thanks to the generosity of my research group principal investigator (Sara Calhim) and the second author’s (Daniel Stec) academic supervisor (Lukasz Michalczyk), who made available to us their spaces and instrumentations, we were able to give a formal name and description to two marvelous tardigrade species.
When describing species, researchers have almost complete freedom to express their creativity or gratitude in bestowing them with names. We decided to honour two people: Dr. Anne Winters, who collected the sample where one of the new species – Macrobiotus annewintersae, was found, and the singer Alexander Rybak with Macrobiotus rybaki.
While routinely examining samples for tardigrades, we stumbled upon tardigrade eggs that didn’t look like any described species. Macrobiotus annewintersae eggs have many conic projections on their surface (called processes) that are topped by about 6 small and stubby tentacles, whereas the processes of Macrobiotus rybaki look like spikes topped with a very tiny dish.
The choice to dedicate the new species to Alexander Rybak is the fruit of our (mine and Daniel’s) passion for the Eurovision Song Contest. We are both fans of this very popular, diverse and cheerful song contest, and we wanted to honour it with a reference to one of its most iconic winners. Rybak’s song Fairytale, which won the 2009 edition, is immediately recognized by any Eurovision Song Contest enthusiast. Our research article, where we describe the two newly found tardigrades,was published in the open-access journal Zoosystematics and Evolutionon 19 May, right in the middle of the semi-finals for this year’s Eurovision Song Contest.
This is not the first instance that a tardigrade species is named after a singer. One species, Barbaria madonnae, was named in 2006 after the singer and performer Madonna.
We hope that naming tardigrade species after popular singers and artists will help popularize them and bring the broad public attention to their conservation.
Vecchi M, Stec D (2021) Integrative descriptions of two new Macrobiotus species (Tardigrada, Eutardigrada, Macrobiotidae) from Mississippi (USA) and Crete (Greece). Zoosystematics and Evolution 97(1): 281-306. https://doi.org/10.3897/zse.97.65280
Editor’s note: The image of Alexander Rybak posted here is credited to NRK P3 under a CC BY-NC-SA 2.0 licence.
Guest blog post by Kennedy “Ned” Rubert-Nason, Caitlin Mandeville and Kirsten Schwarz
Global change is an immediate, accelerating threat to humanity, and its impacts are perpetuated by human activities. Changes such as climate warming, landscape alteration, pollution, resource extraction and depletion, extreme events, biodiversity loss, and spreading of invasive species including diseases, threaten the natural environment and human society. The consequences of these changes are often disproportionately borne by people who have the least political representation. Despite tremendous investment in research aimed at understanding and developing technological solutions to global change threats, implementing effective science-based solutions remains a major challenge.
An article just published in the open-access, peer-reviewed journal Rethinking Ecology explores how translational science, or the process of putting basic research and technological development into use, can bring about the changes in human behavior that are critical to guiding humanity toward a sustainable future. The engine that drives translational science is a theory of change, or strategic plan, which identifies a global change threat, ties it to a goal (usually eliminating or adapting to the threat), and lays out specific actions needed to achieve that goal along with indicators of success. A theory of change that aims to bring about social and structural changes, as required to address global change threats, must embrace relationship-building, collaboration, engagement, commitment, communication, trust, inclusion, equity, transparency, process, and decision framing.
To overcome global change threats, ecologists and other scientists need to prioritize building partnerships with communities that help bring science into practice. These partnerships are critically needed to combat misinformation, build public trust in science, bring about equitable and evidence-informed policies that are accountable to communities’ priorities, and empower people to respond effectively to challenges posed by climate change, pollution, landscape change, extreme events and pandemics.
The authors of the paper identified four priority areas for ecologists to engage in translational science:
garnering public support,
building strong communities,
and protecting natural resources.
While fundamental research remains vital, there needs to be greater emphasis on the communication, policy, education, leadership and role modeling dimensions that help bring the findings from that research into practice. Interdisciplinary scientists like ecologists are particularly well-suited to this line of work, although they can face barriers such as inadequate training, time, funding and institutional support. Lowering these barriers, and creating a culture that values science-based solutions, must be key priorities in future measures aimed at combating global change threats. Many organizations, including the Union of Concerned Scientists and the Ecological Society of America, provide training and support for ecologists to engage more deeply in translational science.
Rubert-Nason K, Casper AMA, Jurjonas M, Mandeville C, Potter R, Schwarz K (2021) Ecologist engagement in translational science is imperative for building resilience to global change threats. Rethinking Ecology 6: 65-92. https://doi.org/10.3897/rethinkingecology.6.64103
Grape seeds have a characteristic oval or pear-like shape. It has been long recognised that this form is variable, and that, in general, wild-type seeds are smaller and more rounded, while the seeds of cultivated varieties tend to be more elongated in one side, or pear-shaped.
Recently, seeds belonging to 38 cultivars stored in the collection of IMIDRA were classified in ten morphological groups, each corresponding to a new morphological model. The models are geometric figures defined by equations, and similarity to each model is evaluated by quantification of percent of the area shared by the two figures, the seed and the model (J index).
The groups thus defined were: Listán Prieto, Albillo Real, Moscatel, Doña Blanca, Hebén, Tortozón, Sylvestris, Teta de Vaca, Airén and de Cuerno.
An article just published in the open-access, peer-reviewed Viticulture Data Journal by the same research groups at IRNASA-CSIC, Department of Mathematics of Salamanca University and IMIDRA, presents an analysis of the curvature – the degree of variation in the points of a curve – in the apex of the cultivars. A set of points along the surface of the seed image are marked and used to obtain the Bézier curves corresponding to seed profiles. The curvature values along the curves are then calculated in Mathematica and represented. Then, the cultivars are classified according to the variation of their curvature and distribution of maximum curvature values. The groups formed based on the curvature analysis are related to the classification based on geometrical figures.
The results show the peduncles of Vitis seeds can be ordered in three groups: 1) Acute, with a unique point of maximum curvature; 2) Plane, with two equivalent points of maximum curvature, and 3) Intermediate. According to this result, the groups based on geometric models are divided by the curvature analysis in two series:
The seeds in most of the cultivars had their pedicels flat at their apex. In consequence, representations of Bézier of their profiles had a plane form with two maximum curvature values. This type was observed in a total of 23 cultivars, including all but one of the 23 cultivars in four groups, and with the addition of Airén. The cultivars with a flat pedicel are predominant in groups Listán Prieto (Listán Prieto and Tortozona Tinta), Albillo Real (Alarije, Albillo Real, Cayetana Blanca, Graciano, Juan García and Tempranillo), eleven of the twelve cultivars of group Moscatel (all of them except Moscatel de grano menudo), the three cultivars of group Doña Blanca (Doña Blanca, Monastrell and Pedro Ximénez) and Airén.
The seeds with an acute apex belong to six cultivars in four groups: Hebén (Macabeo and Zalema, but not Hebén itself), Tortozón (Imperial and Tortozón), Airén (Mazuela) and de Cuerno.
The morphological difference between the seeds of wild grapes and cultivars of Vitis has been known for a long time, but biochemical and structural properties associated with these types remain to be investigated. Considering that lignin is an important component of the cell walls, it is possible that adaptation to agricultural conditions is associated with changes in lignin composition. Pedicel thickening and lignin synthesis may be increased in the cultivars that have their beaks plane in comparison with those varieties that present acute beaks.
Cervantes E, Martín-Gómez JJ, Espinosa-Roldán FE, Muñoz-Organero G, Tocino Á, Cabello Sáenz de Santamaría F (2021) Seed apex curvature in key Spanish grapevine cultivars. Viticulture Data Journal 3: e66478. https://doi.org/10.3897/vdj.3.e66478
A Brazilian network of female zoologists aims to oppose gender disparity in science
Guest blog post by Veronica Slobodian
Scientists are part of a rather sexist society and, therefore, ruled by a rather sexist social conduct. Nevertheless, women scientists attempt to thrive despite all setbacks provided by structural sexism (both explicit and implicit).
Sadly, female scientists are more likely to suffer from harassment, be deprived from recognition for their work, and be more overburdened with household chores compared to their male counterparts. All these situations are being reinforced by social gender stereotypes.
As a result, many women leave academia because of these hindrances and prejudice in a phenomenon known as “leaking pipeline”. To properly address those setbacks, we must first recognize the structural inequalities in academia, and then provide strategies to recruit, retain and promote students and faculty from underrepresented groups.
In a rebuttal to an article published in Nature Communications (AlShebli et al. 2020, now retracted), which suggested that female protégés reap more benefits when mentored by men and, therefore, policies to promote female mentors need to be revisited, our group of female zoologists wrote the opinion paper “Why we shouldn’t blame women for gender disparity in academia: Perspectives of Women in Zoology“, now published in the open-access scientific journal Zoologia. Quickly supported by over 500 signatories from all around the world, the piece soon grew into the Women in Zoology network, which brings together zoologists from underrepresented people in the scientific field groups, especially women.
In this reply, we pointed to the methodological flaws and addressed the inherently problematic conclusions of AlShebli et al. (2020). We also demonstrated the gendered academic settings that systematically prejudices women and presented how some of the current diversity policies are positively changing the zoological field in Brazil. While writing our response, we realized these challenges and aches were in fact much more common in the field, so we decided to broaden the network to encompass all female zoologists who want a more fair and diverse Zoology. So, with the “Women in Zoology” network, our aim is to promote female zoologists, investigate their underrepresentation in Brazilian zoology, and propose policies to balance the situation.
Slobodian V, Soares KDA, Falaschi RL, Prado LR, Camelier P, Guedes TB, Leal LC, Hsiou AS, Del-Rio G, Costa ER, Pereira KRC, D’Angiolella AB, de A Sousa S, Diele-Viegas LM (2021) Why we shouldn’t blame women for gender disparity in academia: perspectives of women in zoology. Zoologia 38: 1-9. https://doi.org/10.3897/zoologia.38.e61968
By 2020, losses of corals have been observed throughout Florida and into the greater Caribbean basin in what turned out to be likely the most lethal recorded case of Stony Coral Tissue Loss Disease. A Perspectives paper, published in the open-access peer-reviewed journal Rethinking Ecology, provides an overview of how Florida ended up in a situation, where the best that could be done is rescuing genetic material from coral species at risk of regional extinction.
Dredging projects conducted in association with coral reefs typically generate concern by environmental groups, resulting in careful monitoring by government agencies. Even though the aim of those dredge projects is to widen or deepen existing ship channels, while minimizing damage to coral reef resources, there are often the intuitive negative assumptions that dredging kills corals.
The recent Port Miami Dredge Project started as an uncomplicated case story. However, significant problems arose, caused by a concurrent and unprecedented coral disease epidemic that killed large numbers of corals, which was initiated following a regional thermal anomaly and coral bleaching event.
The coral disease, known as Stony Coral Tissue Loss Disease (SCTLD), was first observed in September 2014 near Virginia Key, Florida. In roughly six years, the disease has spread throughout Florida and into the greater Caribbean basin. The high prevalence of SCTLD and the resulting high mortality in coral populations, coupled with the large number of susceptible species affected, suggest that this disease outbreak is one of the most lethal ever recorded on contemporary coral reefs. The disease is still presently active and continues to ravage coral reefs throughout the region.
The initial response to this catastrophic disease by resource managers with purview over the ecosystem in Southeast Florida was slow. There is generally a noticeably short window of opportunity to intervene in disease amelioration or eradication in the marine environment. This slow response enabled the disease to spread unchecked. Why was the response to the loss of our coral reefs to a coral disease epidemic such a massive failure? This includes our failure as scientists, regulators, resource managers, local media, and policy makers alike. With this Perspectives paper, published in Rethinking Ecology, my intention was to encapsulate the numerous reasons for our failures during the first few years of the outbreak, reminiscent of the early failures in the U.S. response to the COVID-19 pandemic.
First, the Port Miami dredging project was ongoing when the coral disease epidemic began. Some managers and local environmental groups blamed dredging, rather than SCTLD for the coral losses, reported in the project’s compliance monitoring program. Second, this blame was amplified in the media, because dredging projects are intuitively assumed to be bad for coral reefs. Third, during this same time, the State of Florida prohibited government employees from acknowledging global warming in their work. This was problematic because ocean warming is a proximal cause of many coral diseases.
As a result, some managers ignored the well-known links between warming and coral disease. A consequence of this policy was that the dredging project provided an easy target to blame for the coral mortality noted in the monitoring program, despite convincing data that suggested otherwise.
Specifically, the intensive compliance monitoring program, conducted by trained scientific divers, was statistically significant. SCTLD that was killing massive numbers of corals throughout the region was also killing corals at the dredge site. Further, this was happening in the same proportions and among the same suite of species.
Finally, when the agencies responded to the outbreak, their efforts were too little and much too late to make a meaningful difference. While eradication of the disease was never a possibility, early control measures may have slowed its spread, or allowed for the rescue of significant numbers of large colonies of iconic species. Because of the languid management response to this outbreak, we are now sadly faced with a situation where much of our management efforts are focused on the rescue of genetic material from coral species already at risk of regional extinction.
The delayed response to this SCTLD outbreak in Southeast Florida has many similarities to the COVID-19 pandemic response in the United States and there are lessons learned from both that will improve disease response outcomes in the future, to the benefit of coral reefs and human populations.
Proofreading the text of scientific papers isn’t hard, although it can be tedious. Are all the words spelled correctly? Is all the punctuation correct and in the right place? Is the writing clear and concise, with correct grammar? Are all the cited references listed in the References section, and vice-versa? Are the figure and table citations correct?
Proofreading of text is usually done first by the reviewers, and then finished by the editors and copy editors employed by scientific publishers. A similar kind of proofreading is also done with the small tables of data found in scientific papers, mainly by reviewers familiar with the management and analysis of the data concerned.
But what about proofreading the big volumes of data that are common in biodiversity informatics? Tables with tens or hundreds of thousands of rows and dozens of columns? Who does the proofreading?
Sadly, the answer is usually “No one”. Proofreading large amounts of data isn’t easy and requires special skills and digital tools. The people who compile biodiversity data often lack the skills, the software or the time to properly check what they’ve compiled.
The result is that a great deal of the data made available through biodiversity projects like GBIF is — to be charitable — “messy”. Biodiversity data often needs a lot of patient cleaning by end-users before it’s ready for analysis. To assist end-users, GBIF and other aggregators attach “flags” to each record in the database where an automated check has found a problem. These checks find the most obvious problems amongst the many possible data compilation errors. End-users often have much more work to do after the flags have been dealt with.
In 2017, Pensoft employed a data specialist to proofread the online datasets that are referenced in manuscripts submitted to Pensoft’s journals as data papers. The results of the data-checking are sent to the data paper’s authors, who then edit the datasets. This process has substantially improved many datasets (including those already made available through GBIF) and made them more suitable for digital re-use. At blog publication time, more than 200 datasets have been checked in this way.
Note that a Pensoft data audit does not check the accuracy of the data, for example, whether the authority for a species name is correct, or whether the latitude/longitude for a collecting locality agrees with the verbal description of that locality. For a more or less complete list of what does get checked, see the Data checklist at the bottom of this blog post. These checks are aimed at ensuring that datasets are correctly organised, consistently formatted and easy to move from one digital application to another. The next reader of a digital dataset is likely to be a computer program, not a human. It is essential that the data are structured and formatted, so that they are easily processed by that program and by other programs in the pipeline between the data compiler and the next human user of the data.
Pensoft’s data-checking workflow was previously offered only to authors of data paper manuscripts. It is now available to data compilers generally, with three levels of service:
Basic: the compiler gets a detailed report on what needs fixing
Standard: minor problems are fixed in the dataset and reported
Premium: all detected problems are fixed in collaboration with the data compiler and a report is provided
Because datasets vary so much in size and content, it is not possible to set a price in advance for basic, standard and premium data-checking. To get a quote for a dataset, send an email with a small sample of the data firstname.lastname@example.org.
dataset not UTF-8 encoded
blank or broken records
characters other than letters, numbers, punctuation and plain whitespace
more than one version (the simplest or most correct one) for each character
Windows carriage returns (retained if required)
encoding errors (e.g. “Dum?ril” instead of “Duméril”)
missing data with a variety of representations (blank, “-“, “NA”, “?” etc)
unintended shifts of data items between fields
incorrect or inconsistent formatting of data items (e.g. dates)
different representations of the same data item (pseudo-duplication)
for Darwin Core datasets, incorrect use of Darwin Core fields
data items that are invalid or inappropriate for a field
data items that should be split between fields
data items referring to unexplained entities (e.g. “habitat is type A”)
truncated data items
disagreements between fields within a record
missing, but expected, data items
incorrectly associated data items (e.g. two country codes for the same country)
duplicate records, or partial duplicate records where not needed
For details of the methods used, see the author’s online resources:
The birdcatcher trees – genus Pisonia – are infamous for trapping birds with their super-sticky seed pods that would frequently entangle the body of the ‘victim’. Left flightless, the poor feathered creatures eventually die either from starvation or fatigue, or predators. Similarly notorious are the birdcatcher trees for botanists, who have been baffled by their complicated classification for the last three centuries.
Here’s why myself and graduate student Elson Felipe Rossetto of the Universidade Estadual de Londrina (Brazil) decided to take up the untangling of this issue with our recent taxonomic studies. You can find our research paper published in the open-access scholarly journal PhytoKeys.
We reestablished two genera: Ceodes and Rockia, where both had been previously merged under the name of Pisonia. Now, as a result, there are three distinct lineages of birdcatcher trees from the islands of the Pacific and Indian Oceans: Ceodes, Pisonia, and Rockia.
“Previous molecular studies on Pisonia species from around the world showed that species were clustered into three major groups, and here we assign names for each of them. With this new classification, a large number of the species known as Pisonia will be henceforth named Ceodes. This includes the Parapara (Ceodes brunoniana) and the Birdlime (Ceodes umbellifera) trees, both native to many islands, including Hawaii and New Zealand. They are commonly planted in gardens for their lush and sometimes variegated foliage, as well as their fragrant white flowers. However, the Cabbage tree (Pisonia grandis) will still be technically known as Pisonia.”
adds the study’s lead author Felipe Rossetto.
Birdcatcher trees have generated much controversy in the popular media because of their seed pods (technically called “anthocarps”) secreting a sticky substance that glues them to the feathers of seabirds or other animals for dispersal. Sometimes, though, too many seed pods can harm or kill birds, especially small ones, by weighing them down and rendering them flightless. This macabre practice has led to many controversies and local campaigns aiming to remove the trees, even illegally.
In spite of their forbidding reputation, however, we would like to stress that birdcatcher trees have positive effects on ecosystems and are important components of vegetation, especially for small islands. Sadly, there are many endemic and already endangered species of birdcatcher trees that only exist on a few small islands, where they are effectively placed at the mercy of local people.
Many species of birdcatcher trees are large and, thereby, tolerate harsh environments like seafronts and rocky cliffs, making them prime nesting spots for seabirds. Birdcatcher trees are also ecologically curious and could be regarded as keystone species in small islands, because their soft branches can sustain many types of invertebrates; their flowers are an important food source for bees and ants; their dense leaf litter nourishes the soil; and their roots have intimate interaction with native underground fungi (mycorrhiza).
All in all, clarifying the taxonomy of the birdcatcher trees is the first step to understanding how many species exist and how they relate to each other.
Although most people relate birdcatcher trees with beaches and coastal habitats, there are species that are only found in mountains or rainforests. For example, the species now allocated to the genus Rockia is endemic to the Hawaiian archipelago. These are small trees able to grow in dry to mesic mountain forests. Using our new classification, future studies can explore in detail the hidden diversity of these enigmatic plants, and find out how trees with high dispersal capabilities evolve into species endemic to small island ecosystems.
About the author:
Marcos A. Caraballo-Ortiz is a research associate at the Smithsonian Institution (Washington, D.C., United States). His research interests include plant systematics and ecology, with a focus on flora of the Caribbean Islands. Dr. Caraballo-Ortiz has experience studying the taxonomy of several groups of tropical plants, with a particular interest in neotropical Mistletoes (Loranthaceae, Santalaceae, Viscaceae) and the Four O’Clock family (Nyctaginaceae).
The recognition of the “Ceguaca, la Mujer de los Juncos” locality comes as a result of research work – published last year in Subterranean Biology – which produced the first checklist of bats for Santa Bárbara
Guest blog post by Eduardo Javier Ordoñez-Trejo and Manfredo Alejandro Turcios-Casco
Bat populations are threatened due to fragmentation and loss of their habitats. Meanwhile, dry forests are some of the least studied and most threatened ecosystems in Honduras, and similarly, so have been the caves.
Caves are important reservoirs of species, as they offer perks no other habitat can provide at once: a refuge from predators, inconstant weather, and a critical venue for social interactions, reproduction, hibernation, roosting and nutrients. In order to protect bat populations, the Latin American and Caribbean Web for Bat Conservation (RELCOM) supports the establishment of Areas of Importance for the Conservation of Bats, abbreviated as AICOMS (Spanish for Areas with Importance for the Conservation of Bats) .
Together with biologists of the National Autonomous University of Honduras (UNAH) and local community members, we provided the first ever checklist of bat species in the Dry Forest of Ceguaca, Santa Barbara (Honduras), and described the importance of two caves in the area for bat conservation based on species richness. We published this study last June in Subterranean Biology.
We found that caves in Ceguaca are inhabited by at least 23 bat species of four families, which represents approximately a fifth of all species known from Honduras. Their inhabitants include several threatened species like the hairy-legged vampire bat (Diphylla ecaudata), one of the three existing vampire bats, and rare species with few official records in the area, such as Schmidts’s big-eared bat (Micronycteris schmidtorum). These caves may also represent a critical site for roosting and nursing. During our study, we managed to record pregnant and lactating females of several species, as well as reproductive males.
“It feels wonderful to see that our work has had great results and that with our efforts, we established an area where bats will be protected and studied. This certification also includes the name of Roberto Castellano, an elder member of the community of Ceguaca, who helped us during the fieldwork as our guide. He was a great conservationist of this area and protector of the caves. Unfortunately, he passed away during the study, however, due to his enormous contribution, we dedicated our article to him and included him as part of this AICOM success.”
José Alejandro Soler Orellana, co-author of the study.
Using what we learned in Ceguaca’s caves, we approached the Program for Bat Conservation of Honduras (PCMH) and showed them the evidence the locality was indeed a precious place with a spectacular bat diversity. Consequently, thanks to our collaboration with the PCMH, the site was effectively declared as an Area of Importance for the Conservation of Bats by RELCOM on 6th March 2020.
This is an enormous step for bat conservation in the country. Bat conservation efforts should focus on studying and protecting these and other important habitats. We also need to make sure that local people appreciate the important role the bats play in the ecosystem.
Turcios-Casco MA, Mazier DIO, Orellana JAS, Ávila-Palma HD, Trejo EJO (2019) Two caves in western Honduras are important for bat conservation: first checklist of bats in Santa Bárbara. Subterranean Biology 30: 41–55. https://doi.org/10.3897/subtbiol.30.35420